AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690

From: Catein Catherine <>
Date: Wed, 24 Oct 2007 20:04:42 +0800

Dear Prof. Case and other researchers,
I am reading an article published by Prof. Case in 1988, regardng the use of the PMF to calculate the rate constant for a reaction pathway. I am fresh to this area, following, I could like to ask for your professional advices, please kindly help.
(1) I noted the average absolute value of the crossing velocity was listed in the second column of the Table III. Could you please kindly instruct me how to get these numbers from the PMF result?
(2) What is the use of average velocity at the top of the barrier and equation (6) regarding the reduced masses, as it does not seem to appear in equation (5) of the paper for the calculation of kTST.
(3) Related to the question (2), I cannot reproduce the kTST listed in the fifth column of Table III. I should have missed something very important, as I have only time 2.594e4 with 3.737e-10 according to equation (5) of the paper.
(4) I noted some publication find the plateau value of transmission coefficient, what additional simulation or calculation should I do the get this values done? Is it a must to do this calculation if similar binding site and only qualiative discussion would be make?
Sorry to have asked so many questions, I hope you could not mind to give me a hand and teach me what should I do next? Thank you very much in advanced.
Best regards
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Received on Sun Oct 28 2007 - 06:07:06 PDT
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